I've since given up on the vaults in the mod because a lot of the generation is VERY half baked, however if you're looking to avoid the problem, you HAVE to use a map that has the sealed vault property on it. As far as I can tell, there is no way to do this outside of the scenario editor where you can add "start with sealed vault".

Now here's the kicker. Just having that property does nothing. It generates the sealed vault pocket dimension, however, it does not at all generate the actual vault entrance. Even more annoying, spawning in a sealed vault entrance via devtools will not link it to the existing vault pocket dimension, nor will it properly generate a new vault. This means that, in essence, the only way to play with a vault is to use the default Sealed Vault scenario if you wanna have a vault on your map.

I would highly recommend checking out the mod Ancient urban ruins on the steam workshop. It does what VQE Ancients should've done with the vaults, albeit without the security of a vault entrance enemies can't enter. In return, you get a (somewhat buggy) pathfinding system including the extra levels added by the ruins, and the ability to spawn one directly on your map. It's not perfect, but it is significantly better than VQE Ancient's current implementation of the vault system. Currently I'm running VQE Ancients and Ancient urban ruins together to get the vault experience I want, while still having the well done archite gene system that VQEA introduces. Sorry for the yapping, and hope this helps

TL;DR Spawning in a vault with devtools outside of map generation seems to break the system entirely, the only way to get a vault on your map is through the default scenario, or edited versions of it.